Intro to Cell Biology Lecture Notes Fall 2024 PDF

Intro to Cell Biology September 4, 2024 Dr. Dana Pape-Zambito [email protected] All images from Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company, unless otherwise noted...

Intro to Cell Biology September 4, 2024 Dr. Dana Pape-Zambito [email protected] All images from Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company, unless otherwise noted 1 Learning Objectives (1-6 = Chapter 1) 1. Define characteristics of living organisms. Explain the central dogma of biology. 2. Distinguish between prokaryotes and eukaryotes. Give examples of each. 3. Identify cellular organelles/structures in prokaryotic, plant and animal cells and explain their function within the cell. 4. Describe important components of each structure/organelle and explain why these structures are necessary for the organelle’s function. 5. Outline the evolution of mitochondria and chloroplasts and cite the evidence for these origins (i.e. the endosymbiotic theory). 6. Compare and contrast light (conventional and fluorescent) and electron microscopy including requirements for each technique, which cells/organelles/structures can be viewed, resolution, and limitations of each technique. 14 Learning Objectives (7-10; Chapter 2) 7. Use the periodic table to determine the number of valence electrons in an atom and explain how valence electrons lead to the chemical reactivity of atoms. 8. Explain the difference between ionic, covalent, and hydrogen bonds, as well as Van der Waal interactions. Give examples of each. 9. Compare and contrast the terms hydrophilic, hydrophobic, polar, non-polar, lipophilic, lipophobic, amphipathic. Give examples of each. 10. Recognize the chemical structures and characteristics of the major cellular macromolecules (carbohydrates, proteins, lipids, and nucleic acids). Identify the monomer units required to build oligomer or polymer macromolecular structures. Explain where you would expect to find these macromolecules within prokaryotic and eukaryotic cells. 15  Chapter 1 - Cells the Fundamental Units of Life Image accessed from: 16 https://moosmosis.org/2018/09/01/cornerstones-of-microbiology-robert-hooke-anton-van-leeuwenhoek/ Think, Pair, Share - How do we define life? 19  LO #1 Unity and Diversity of Life Basic unit of life = cell Cells are bound by membranes and contain genetic material Cells can self-replicate 20  LO #1 Central Dogma Required before cell division DNA ↓ mRNA ↓ Protein Required to perform cellular functions 21  LO #2 22 Image from: https://www.sciencefacts.net/prokaryotes-vs-eukaryotes.html Prokaryote or Eukaryote? Bacteria, Archaea, Plant, Animal, or Protist? LO #2 23  LO #1&2 Test your knowledge - True or False? Prokaryotes are larger than eukaryotes. False The hereditary information is passed on through proteins. False Protists are prokaryotes. False Bacterial DNA is found within the cytoplasm. True 25 Prokaryotes and eukaryotes share all of the following EXCEPT? A. Ribosomes B. Cell Membrane C. DNA D. RNA E. Nucleus 28  Activity - Work with your group members to identify the cellular structures. Indicate the functions of each structure. (8 min) LO #3 & 4 Image from Campbell Biology, Pearson publishers 29 LO #3 & 4 31  LO #3 & 4 Image from: https://www.earthslab.com/physiology/structure-cell-membrane-cytoplasm-organelles/ 32 Study Guide - Fill out on your own to study LO #3 & 4 Organelle Function Structural What would happen if this components structure did not function properly? 33  Mitochondria and Endosymbiotic Theory - Recap chloroplasts evolved from the engulfment of bacteria. There were 2 separate engulfment events. Evidence: - Size of organelles similar to size of prokaryotic cells - Double membranes - DNA - Divide to reproduce LO #5 35 We can use light and electron microscopes to visualize cells LO #6 36  LO #6 Light microscopy was used to obtain these images 37  Light Microscopy - uses light, lenses, and dyes to see live and fixed cells A) Bright field B) Phase-contrast C) Interference-contrast Note: Dye not required LO #6 38  Fluorescence microscopy - uses light, filters, and fluorescent dyes to see live and fixed cells Top Row = Widefield or standard fluorescence microscopy Bottom Row = Confocal microscopy (more common today) Note: Dye required What is difference between the rows? Image from: LO #6 https://www.olympus-lifescience.com/en/microscope-resource/primer/techniques/confocal/confocalintro/ 39 Electron microscopy (EM) - uses an electron beam, lenses, and stains or resins to see fixed specimens at high magnification If you were given an EM image of a cell, could you identify the structures? Homework 1 will help with this! Scanning EM in 3D!! LO #6 Transmission EM 40  LO #6 Compare and contrast microscopy techniques Light Fluorescent Electron Illumination Source Light Light Electrons Specimen type Live or Dead (fixed) Live or Dead (fixed) Dead (fixed) only Dyes or Stains Not required, but can Fluorescent dye Heavy metal dye be used required, multiple required colors OK. Magnification Power 40x - 1000x 12.5x - 1500x 100,000x - 300,000x 41 200 µm 200 nm 42 If you wanted to see how a single microtubule in a cell changes when exposed to a drug, which type of microscopy would you use? A. Light microscopy without any stains or special filters B. Light microscopy using interference phase contrast filters C. Confocal fluorescence microscopy D. Scanning electron microscopy E. Transmission electron microscopy 44 If you wanted to see how a single microtubule in a cell changes when exposed to a drug, which type of microscopy would you use? A. Light microscopy without any stains or special filters B. Light microscopy using interference phase contrast filters C. Confocal fluorescence microscopy D. Scanning electron microscopy E. Transmission electron microscopy 45  Review - Reading the Periodic Table LO #7 Atomic number determined by # of protons. Atomic mass = mass of protons + neutrons Electrically neutral atoms have equal numbers of protons and electrons. = mass of protons + neutrons 47  Review - the Periodic Table LO #7 Chemical reactivity determined by the # of electrons. Down rows = # of electron shells. First shell = 2 e-, additional shells hold 8 e-. Across columns = increasing # of electrons. 48  Test your knowledge LO #7 How many total electrons does Mg have? 12 How many electrons are in Mg’s outer valence shell? 2 How many electrons does Mg need to fill its outer shell? 6 49  LO #7 Isotopes - # of Protons are similar, but neutrons are different Radioisotopes are powerful scientific tools C12 and C14 - radioisotope dating Cancer detection (see right) Brain, kidney, and bladder take up and metabolize the radioisotope normally. Devoogdt et al., 2012. ResearchGate. 50 Figure 1  Understanding chemical bonding and valency LO #8 Covalent vs. ionic bonds Covalent bonding - electrons shared Non-polar covalent bond (a) = equal sharing of electrons Polar covalent bond (b) = unequal sharing of electrons Ionic bonding (c) - electrons transferred https://www.youtube.com/watch?v=OTgpN62ou24 Valency video - watch outside of class if you need additional clarification https://www.youtube.com/watch?v=lVSF2lP4oBA 51  LO #8 Hydrogen bonding - weak bonds that form between different molecules Water molecule, not mickey mouse Hydrogen bond, dashed line Polar covalent bond, solid line Hydrogen bond 53 Images from Campbell Biology, Pearson Education Inc.  LO #8 Van der Waals = Weak Interactions But can be powerful when many work together Image from: http://www.sci-news.com/othersciences/physicalchemistry/wave-lik e-nature-van-der-waals-forces-03717.html 54  LO #10 A) Identify the macromolecules shown above (you don’t need to identify the specific molecule, rather just indicate the type of macromolecule). SUGAR OR CARBOHYDRATE B) Give an example of this macromolecule that you might expect to find in your body (ex. insulin) GLUCOSE, GLYCOGEN, (STARCH, CELLULOSE IN PLANTS) C) Explain how you knew what macromolecule it was. GENERAL MOLECULAR FORMULA = CN(H2O)N D) What individual monomers make up the larger oligomer or polymer? MONOSACCHARIDE E) Identify the individual monomers in these structures. SEE BLUE BOX F) Describe where you would expect to find these macromolecules in prokaryotic, plant, and animal cells. CELL WALLS (PROKARYOTES, PLANTS, FUNGI), CREATED IN CHLOROPLAST, CATABOLIZED IN MITOCHONDRIA, STARCH IN PLANT VACUOLES, GLYCOGEN IN MUSCLES, MODIFIES PROTEINS AND LIPIDS. 58  LO #10 AMINO ACID A) Identify the macromolecules shown above (you don’t need to identify the specific molecule, rather just indicate the type of macromolecule). PROTEIN - SHOWN ABOVE IS A POLYPEPTIDE. B) Give an example of this macromolecule that you might expect to find in your body (ex. insulin). INSULIN, GROWTH HORMONE, ACTIN, MYOSIN, ETC. C) Explain how you knew what macromolecule it was. CONTAINS -CH + AMINO GROUP (-NH2) + CARBOXYLIC ACID GROUP (-COOH) + R GROUP (UNIQUE FOR EACH AMINO ACID). D) What individual monomers make up the larger oligomer or polymer? AMINO ACIDS E) Identify the individual monomers in these structures. SEE BLUE BOXES ABOVE. NOTE H2O IS LOST FROM -NH2 AND -COOH DURING POLYMERIZATION (condensation reaction for each monomer added). F) Describe where you would expect to find these macromolecules in prokaryotic, plant, and animal cells. RECEPTORS, TRANSPORT PROTEINS (IN MEMBRANE), MOTOR PROTEINS (IN CYTOPLASM), CRITICAL STRUCTURES IN MANY CELL ORGANELLES. 60  LO #10 Proteins are translated directionally. They have an N-terminal end and a C-terminal end. Translation starts at the N-terminal end and proceeds to the C-terminal end. 61  LO #10 NUCLEOTIDE A) Identify the macromolecules shown above (you don’t need to identify the specific molecule, rather just indicate the type of macromolecule). NUCLEIC ACID B) Give an example of this macromolecule that you might expect to find in your body (ex. insulin). DNA OR RNA C) Explain how you knew what macromolecule it was. CONTAINS A SUGAR + PHOSPHATE BACKBONE, AND NITROGENOUS BASE. D) What individual monomers make up the larger oligomer or polymer? NUCLEOTIDES. E) Identify the individual monomers in these structures. SEE BLUE BOX. F) Describe where you would expect to find these macromolecules in prokaryotic, plant, and animal cells. IN PROKARYOTES - IN THE CYTOPLASM IN THE NUCLEOID REGION, DNA IN NUCLEUS OF EUKARYOTES, RNA IN NUCLEUS OR CYTOPLASM. 63  LO #10 FATTY ACID TAIL A) Identify the macromolecules shown above (you don’t need to identify the specific molecule, rather just indicate the type of macromolecule). LIPID - THIS IS A PHOSPHOLIPID B) Give an example of this macromolecule that you might expect to find in your body (ex. insulin). PHOSPHOLIPIDS, TRIGLYCERIDE, STEROID HORMONES ARE ALL LIPID MACROMOLECULES. C) Explain how you knew what macromolecule it was. 2 HYDROCARBON TAILS WITH PHOSPHATE HEAD (PHOSPHOLIPID). ALL LIPIDS HAVE HYDROCARBON PORTIONS THAT ARE HYDROPHOBIC. D) What individual monomers make up the larger oligomer or polymer? PHOSPHOLIPIDS AND TRIGLYCERIDES HAVE FATTY ACID TAILS, BUT STEROIDS DO NOT. SO THERE IS NOT A SINGLE MONOMER. E) Identify the individual monomers in these structures. SEE ANSWER TO D) ABOVE. F) Describe where you would expect to find these macromolecules in prokaryotic, plant, and animal cells. CELL MEMBRANE, MEMBRANE BOUND ORGANELLES. 65  LO #10 Imagine you are a scientist who needs to distinguish between a protein and a nucleic acid. Which element would you use an isotope for if you wanted to label and trace a nucleic acid (vs. a protein). Explain why. PHOSPHOROUS - B/C NUCLEIC ACIDS HAVE PHOSPHATE GROUPS, BUT PROTEINS DO NOT. Which element would you use an isotope for if you wanted to label and trace a protein (vs. nucleic acid). Explain why. SULFUR - B/C PROTEINS HAVE SULFUR (AMINO ACIDS CYSTEINE AND METHIONINE) THAT STABILIZE SECONDARY, TERTIARY, AND QUATERNARY STRUCTURE. NUCLEIC ACIDS DO NOT CONTAIN SULFUR. 67